#!/bin/bash

#SBATCH -J 32core_IQTree-parti_15cephala_nozorro        # Job name 
#SBATCH -o 32core_IQTree-parti_15cephala_nozorro.%A.out                    # File to which stdout will be written
#SBATCH -e 32core_IQTree-parti_15cephala_nozorro.%A.err                    # File to which stderr will be written
#SBATCH --mail-type=ALL                         # BEGIN,END,ALL
#SBATCH --mail-user=vknutson@g.harvard.edu   # Email address
#SBATCH -n 1                                    # Number of tasks
#SBATCH -c 32                                   # Number of threads/processors/cpus per task
#SBATCH -t 4-00:00                             # Runtime in DD-HH:MM
#SBATCH --mem-per-cpu 2500                      # Memory for all cores in Mbytes (--mem-per-cpu for MPI jobs)
#SBATCH -p holygiribet,shared     #Partition shared, serial_requeue, unrestricted, interact
#SBATCH --contiguous # In partitioned analyses

module purge
module load gcc/7.1.0-fasrc01 openmpi/2.1.0-fasrc02 iqtree/1.5.5-fasrc02

#32 cores
srun -n $SLURM_NTASKS -c $SLURM_CPUS_PER_TASK --mpi=pmi2 --export=ALL iqtree-omp-mpi -nt $SLURM_CPUS_PER_TASK \
-st AA -ninit 10 -bb 1500 -msub nuclear -s ../15cephala_nozorro.phy -sp partifile_15cephala_nozorro.txt \
-m MFP+MERGE -rcluster 10 -madd LG4M,LG4X -mrate G,R,E

# -sp (partition accounting for heterotachy)
# -o for outgroup name e.g. -o $3
